ArticleThe Journal of chemical physics2013
Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.
Article in The Journal of chemical physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed.
- Compartmental exchange regulates steady states and stochastic switching of a phosphorylation network.Biophysical journal · 2024Article
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].Living journal of computational molecular science · 2023Article
- Simulation of receptor triggering by kinetic segregation shows role of oligomers and close contacts.Biophysical journal · 2022Article
- Predicting pathological von Willebrand factor unraveling in elongational flow.Biophysical journal · 2021Article
- Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling.ACS omega · 2020Article
- Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" Analysis.Journal of chemical theory and computation · 2020Article
- Automatic error control during forward flux sampling of rare events in master equation models.The Journal of chemical physics · 2020Article
- OPTIMIZING WEIGHTED ENSEMBLE SAMPLING OF STEADY STATES.Multiscale modeling & simulation : a SIAM interdisciplinary journal · 2020Article
- Data-Driven Method for Efficient Characterization of Rare Event Probabilities in Biochemical Systems.Bulletin of mathematical biology · 2019Article
- Computational Estimation of Microsecond to Second Atomistic Folding Times.Journal of the American Chemical Society · 2019Article
- MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework.Methods in molecular biology (Clifton, N.J.) · 2019Article
- A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0].Living journal of computational molecular science · 2019Article
- Rare-event sampling of epigenetic landscapes and phenotype transitions.PLoS computational biology · 2018Article
- Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.Annual review of biophysics · 2017Review
- Path-sampling strategies for simulating rare events in biomolecular systems.Current opinion in structural biology · 2017Review
- SParSE++: improved event-based stochastic parameter search.BMC systems biology · 2016Article
- Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide.The journal of physical chemistry letters · 2016Article
- Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.PLoS computational biology · 2016Article
- ACCURATE CHEMICAL MASTER EQUATION SOLUTION USING MULTI-FINITE BUFFERS.Multiscale modeling & simulation : a SIAM interdisciplinary journal · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
We apply the "weighted ensemble" (WE) simulation strategy, previously employed in the context of molecular dynamics simulations, to a series of systems-biology models that range in complexity from a one-dimensional system to a system with 354 species and 3680 reactions. WE is relatively easy to implement, does not require extensive hand-tuning of parameters, does not depend on the details of the simulation algorithm, and can facilitate the simulation of extremely rare events. For the coupled stochastic reaction systems we study, WE is able to produce accurate and efficient approximations of the joint probability distribution for all chemical species for all time t. WE is also able to efficiently extract mean first passage times for the systems, via the construction of a steady-state condition with feedback. In all cases studied here, WE results agree with independent "brute-force" calculations, but significantly enhance the precision with which rare or slow processes can be characterized. Speedups over "brute-force" in sampling rare events via the Gillespie direct Stochastic Simulation Algorithm range from ~10(12) to ~10(18) for characterizing rare states in a distribution, and ~10(2) to ~10(4) for finding mean first passage times.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.